Welcome to the GenomeWeb
Comparative Genome Databases

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This is a collection of comparative genome databases.

[info] Mammalian Homology and Comparative Maps
[info] The dysmorphic human and mouse homology database
[info] Human/Mouse Homology Relationships
[info] Homologous Unigenes between Human and Mouse
[info] XLocus
[info] The Homeobox Page
[info] XREFdb
[info] Online Mendelian Inheritance In Animals (OMIA)
[info] Online Cytogenetics of Animals (OCOA)
[info] Database Of Genome Sizes (DOGS)
[info] INRA comparative homology database
[info] Mutation Spectra Database
[info] GeneCensus Genome Comparisons
[info] Completed genomes search and analysis

Detailed information on the above options

Mammalian Homology and Comparative Maps
MGD contains homology information for mouse, human and over 70 other mammalian species. By far, most of the information for homologies is extracted from the published scientific literature. In general, these papers explicitly report homology relationships and MGD reflects that published information. (See information on criteria used for establishing homology.)

An homology record shows the symbol, species, chromosome, cM position, cytogenetic band, symbol and accession ID for each gene in the set of homologies. In addition, links to other mammalian databases are provided where possible. MGD homology records may link to GDB, BovMap, PiGBASE, RATMAP, or SheepBase. or ArkDB. In addition, the Homology menu provides a link to mouse/Drosophila homologies extracted from data maintained by Michael Ashburner at FlyBase.

The dysmorphic human and mouse homology database
This consists of three separate databases of human and mouse malformation syndromes together with a database of mouse/human syntenic regions. The mouse and human malformation databases are linked together through the chromosome synteny database. The purpose of the system is to allow retrieval of syndromes according to detailed phenotypic descriptions and to be able to carry out homology searches for the purpose of gene mapping. Thus the database can be used to search for human or mouse malformation syndromes in different ways:-

Human/Mouse Homology Relationships
This is the Seldin/Debry Human/Mouse Homology Map, a table comparing genes in homologous segments of DNA from human and mouse sources, sorted by position in each genome. The authors did not include pseudogenes, members of multigene families where specific homology relationships could not be determined, nor any other genes for which homology was in doubt.

Homologous Unigenes between Human and Mouse
~650 correlated human and mouse UniGene cluster pairs.

Human Unigene info was from ftp://ftp.ncbi.nlm.nih.gov/, The version was"UniGene Build #42"; the mouse version was"UniGene Build #21". In NCBI's repository/unigene directory, the files are called "Hs.data" and"Mm.data". The file format is in kind of "object-oriented" style, and I wrote a Perl program to convert each of them into two relational tables. The matching was done by joining mouse and human tables on the"GENE" field - mouse and human unigenes with the same gene names were retrieved.

So now you see the result is a limited set of homologous genes between them (those that have the same GENE symble). Other possible homologous genes were ignored (those that do not yet have gene names, or have different gene names).

The XLocus database is an experimental attempt to link several genome databases together. It is a cross-referencing database for gene-to-gene links.

The Homeobox Page
This specificially deals with issues about homeobox genes, (in particular about classification/evolution).

XREFdb is a component of an effort to cross-reference the genetics of model organisms with mammalian phenotypes and expedite the discovery of genes mutated in human disease states. The database has been designed to interact with the community, communicating to participating laboratories similarity search results identifying significant matches between protein sequences of interest (both published and unpublished) and mammalian peptide sequences predicted by the translation of Expressed Sequence Tags (ESTs).

In addition, this effort will determine mouse and human map positions for those ESTs which are most significantly matched by protein sequences from the budding yeast Saccharomyces cerevisiae, many of which are associated gene function data. The map data will effectively establish cross-references between yeast genes (and related genes in other model organisms) and mammalian phenotypes via the phenotype-rich mouse and human maps, offering the possibility for profound discoveries in human disease research. If any EST map data become available which are relevant to the query set of an XREFdb accountholder, those data will be automatically reported to that laboratory on a non- collaborative basis.

Online Mendelian Inheritance In Animals (OMIA)
The Online Mendelian Inheritance in Animals (OMIA) is a database of the genes and phenes that have been documented in a wide range of animal species other than those for which databases already exist (human, rat and mouse).

It contains references to publications on any trait or disorder for which familial inheritance has been claimed. It does not contain sequence data. Each reference has been indexed to one or more phenes and/or genes, and to species. It contains gene information, synonyms for phenes, summaries of current knowledge, clinical and diagnostic features and cross-references to other knowledgebases.

Online Cytogenetics of Animals (OCOA)
OCOA is a bibliographic resource: it contains references to the literature on the cytogenetics of animals, but at this early stage, it does NOT contain any images of karyotypes (either normal or abnormal).

Database Of Genome Sizes (DOGS)
A simple listing sizes of gemones of various organisms.

INRA comparative homology database
Each table lists the references on the species you asked in the three INRA databases : BOVMAP ( BTA ), GOATMAP ( CHI ), HORSEMAP ( ECA ), or in the specific database you come from. The tables list, on the left part, the loci in the database ( ex : in BOVMAP ), with : symbol, localization and name. Click on symbol or localization to enter in the database ( ex : BOVMAP ) and access details about this locus. On the right part are listed the loci ( localization ) in database mapping the species you asked ( ex : GDB for human ). Click on this localization to access distant database and view detail about locus.

Mutation Spectra Database
This database consists of over 24 000 mutations in 18 viral, bacterial, yeast or mammalian genes. The data are grouped as sets of DNA base sequence changes or spectra caused by a particular mutagen under defined conditions.

GeneCensus Genome Comparisons
GeneCensus is intended to give a comprehensive statistical accounting of protein structural features in genomes, and in the sequence databanks -- in the sense of a demographic census.

Completed genomes search and analysis
A new era in biology has begun with the availability of the complete and near complete genomes. All those involved are to be congratulated for these full genetic blueprints. We have created the following pages with the aim of making this information useful and readily available to the community.

Any Comments, Questions? Support@hgmp.mrc.ac.uk